a2m2html output for tmp.a2m

Citations (SAM, SAM-T99, HMMs)

R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting remote protein homologies, Bioinformatics 14(10):846-856, 1998.
A. Krogh et al., Hidden Markov models in computational biology: Applications to protein modeling, JMB 235:1501-1531, Feb 1994.

Sequence numbers correspond to the following labels:

- T0471
- gi|15679018|ref|NP_276135.1|_1:133 hypothetical protein MTH1000 [Methanothermobacter thermautotrophicus str. Delta H]
- gi|13634000|sp|O27081|YA00_METTH UPF0146 protein MTH_1000 [Taxonomy]
- gi|2622083|gb|AAB85479.1| conserved protein [Methanothermobacter thermautotrophicus str. Delta H]
- gi|159904727|ref|YP_001548389.1|_7:134 Protein of unknown function UPF0146 [Methanococcus maripaludis C6]
- gi|159886220|gb|ABX01157.1| Protein of unknown function UPF0146 [Methanococcus maripaludis C6]
- gi|45358120|ref|NP_987677.1|_8:134 hypothetical protein MMP0557 [Methanococcus maripaludis S2]
- gi|44920877|emb|CAF30113.1| conserved hypothetical archaeal protein [Methanococcus maripaludis S2]
- gi|134046084|ref|YP_001097570.1|_8:134 hypothetical protein MmarC5_1050 [Methanococcus maripaludis C5]
- gi|132663709|gb|ABO35355.1| Protein of unknown function UPF0146 [Methanococcus maripaludis C5]
- gi|150403491|ref|YP_001330785.1|_9:134 hypothetical protein MmarC7_1576 [Methanococcus maripaludis C7]
- gi|150034521|gb|ABR66634.1| Protein of unknown function UPF0146 [Methanococcus maripaludis C7]
- gi|154150618|ref|YP_001404236.1|_6:136 Protein of unknown function UPF0146 [Candidatus Methanoregula boonei 6A8]
- gi|153999170|gb|ABS55593.1| Protein of unknown function UPF0146 [Candidatus Methanoregula boonei 6A8]
- gi|2128443|pir||H64385_19:142 hypothetical protein MJ0688 - Methanococcus jannaschii [Taxonomy]
- gi|15668869|ref|NP_247672.1|_19:142 hypothetical protein MJ0688 [Methanocaldococcus jannaschii DSM 2661]
- gi|2826309|gb|AAB98683.1| conserved hypothetical protein [Methanocaldococcus jannaschii DSM 2661]
- gi|13638552|sp|Q58101|Y688_METJA_9:132 UPF0146 protein MJ0688 [Taxonomy]
- gi|14590142|ref|NP_142206.1|_8:129 hypothetical protein PH0209 [Pyrococcus horikoshii OT3]
- gi|13634005|sp|O57948|Y209_PYRHO UPF0146 protein PH0209 [Taxonomy]
- gi|3256595|dbj|BAA29278.1| 131aa long hypothetical protein [Pyrococcus horikoshii OT3]
- gi|150400175|ref|YP_001323942.1|_10:135 hypothetical protein Mevan_1435 [Methanococcus vannielii SB]
- gi|150012878|gb|ABR55330.1| Protein of unknown function UPF0146 [Methanococcus vannielii SB]
- gi|150401067|ref|YP_001324833.1|_23:141 hypothetical protein Maeo_0637 [Methanococcus aeolicus Nankai-3]
- gi|150013770|gb|ABR56221.1| Protein of unknown function UPF0146 [Methanococcus aeolicus Nankai-3]
- gi|14520412|ref|NP_125887.1|_8:129 hypothetical protein PAB2224 [Pyrococcus abyssi GE5]
- gi|13634072|sp|Q9V280|Y194_PYRAB UPF0146 protein PYRAB01940 [Taxonomy]
- gi|5457627|emb|CAB49118.1| Hypothetical protein [Pyrococcus abyssi GE5]
- gi|126178780|ref|YP_001046745.1|_6:131 Protein of unknown function UPF0146 [Methanoculleus marisnigri JR1]
- gi|125861574|gb|ABN56763.1| Protein of unknown function UPF0146 [Methanoculleus marisnigri JR1]
- gi|13634010|sp|P58014|Y73A_ARCFU_7:123 UPF0146 protein AF_0739.1 [Taxonomy]
- gi|11500020|ref|NP_071266.1|_7:121 hypothetical protein AF0740a [Archaeoglobus fulgidus DSM 4304]
- gi|88602206|ref|YP_502384.1|_6:127 hypothetical protein Mhun_0915 [Methanospirillum hungatei JF-1]
- gi|88187668|gb|ABD40665.1| conserved hypothetical protein [Methanospirillum hungatei JF-1]
- gi|163798600|ref|ZP_02192507.1|_24:141 Protein of unknown function UPF0146 [Methanococcus voltae A3]
- gi|158972607|gb|EDP40075.1| Protein of unknown function UPF0146 [Methanococcus voltae A3]
- gi|147921116|ref|YP_685073.1|_8:122 hypothetical protein RCIX280 [uncultured methanogenic archaeon RC-I]
- gi|56295552|emb|CAH04795.1| conserved hypothetical protein [uncultured archaeon]
- gi|110620469|emb|CAJ35747.1| conserved hypothetical protein [uncultured methanogenic archaeon RC-I]
- gi|148642954|ref|YP_001273467.1|_5:118 hypothetical protein Msm_0894 [Methanobrevibacter smithii ATCC 35061]
- gi|148551971|gb|ABQ87099.1| conserved hypothetical protein Msm_0894 [Methanobrevibacter smithii ATCC 35061]
- gi|57641711|ref|YP_184189.1|_10:129 hypothetical protein TK1776 [Thermococcus kodakarensis KOD1]
- gi|57160035|dbj|BAD85965.1| hypothetical protein, conserved, UPF0146 family [Thermococcus kodakarensis KOD1]
- gi|84489995|ref|YP_448227.1|_6:116 hypothetical protein Msp_1203 [Methanosphaera stadtmanae DSM 3091]
- gi|84373314|gb|ABC57584.1| conserved hypothetical protein [Methanosphaera stadtmanae DSM 3091]
- gi|18976495|ref|NP_577852.1|_9:130 hypothetical protein PF0123 [Pyrococcus furiosus DSM 3638]
- gi|30580629|sp|Q8U4G5|Y123_PYRFU UPF0146 protein PF0123 [Taxonomy]
- gi|18892040|gb|AAL80247.1| putative methyltransferase [Pyrococcus furiosus DSM 3638]
- gi|124485264|ref|YP_001029880.1|_16:135 hypothetical protein Mlab_0437 [Methanocorpusculum labreanum Z]
- gi|124362805|gb|ABN06613.1| Protein of unknown function UPF0146 [Methanocorpusculum labreanum Z]
- gi|76801038|ref|YP_326046.1|_4:125 hypothetical protein NP0772A [Natronomonas pharaonis DSM 2160]
- gi|76556903|emb|CAI48477.1| conserved hypothetical protein [Natronomonas pharaonis DSM 2160]
- gi|116754427|ref|YP_843545.1|_5:108 Protein of unknown function UPF0146 [Methanosaeta thermophila PT]
- gi|116665878|gb|ABK14905.1| Protein of unknown function UPF0146 [Methanosaeta thermophila PT]
- gi|110667337|ref|YP_657148.1|_2:128 hypothetical protein HQ1375A [Haloquadratum walsbyi DSM 16790]
- gi|109625084|emb|CAJ51503.1| conserved hypothetical protein [Haloquadratum walsbyi DSM 16790]
- gi|16554522|ref|NP_444246.1|_15:110 hypothetical protein VNG2608a [Halobacterium sp. NRC-1]
- gi|169237103|ref|YP_001690303.1| conserved hypothetical protein [Halobacterium salinarum R1]
- gi|13634038|sp|P58015|Y2609_HALSA UPF0146 protein VNG_2609C [Taxonomy]
- gi|167728169|emb|CAP14957.1| conserved hypothetical protein [Halobacterium salinarum R1]

              10        20        30             40                   5
              |         |         |              |                    
   1 MWNDLAVYIIRCSGPGTRVVEVGAGRFLYVSDYIRKH.....SKVDLVLTD...IK...P.....
   2 MWNDLAVYIIRCSGPGTRVVEVGAGRFLYVSDYIRKH.....SKVDLVLTD...IK...P.....
   3 ---YIDEHYRNLKNKGLKVAELGIGFYFNNAKKLKEI.....GFDVIVIDI...NK...Nav7ke
   4 ----IDENYQNLKNNGLKIAELGIGFYFNNAKKLKDS.....GFDVIVIDI...NK...Nav7kd
   5 ----INENYGHIKNKGLKVAELGIGFYFDNAKKLKDS.....GFEVIVIDI...NK...Nav7ke
   6 -----DENYSDIKNKELKIAELGIGFYFDNAKKLKDS.....GFDVIVIDI...NK...Nav7ek
   7 --HIEHCCGVYIAQHYTNPVEIGVGSNPDAAQCIHEA.....GIPVRARDVracNL...P.....
   8 -----FIKKFAEENNCKKIAEIGIGFKFDVARELSKYxd6aiDINEKAIEK...AK...L.....
   9 -----FIKKFAEENNCKKIAEIGIGFKFDVARELSKYfd6aiDINEKAIEK...AK...L.....
  10 -----FIKKFAEENNCKKIAEIGIGFKFDVARELSKYfd6aiDINEKAIEK...AK...L.....
  11 ---------IAREIRRGKIVEIGVGFYLEVAKRLRES.....GIDILVVDI...NE...Kai7rk
  12 -----NNYSHLKNNSKIVVAEIGIGFYVEISKKMQKS.....GFNVIAIDS...NE...Kav7fq
  13 ------------NSESFKIIEIGVGYYFNIAKSLNNH.....ENLNLIVID...AN...Nda8kk
  14 ---------IAREVKKGKVIEVGIGFYTRIAKRLKEL.....GFDVLAIDI...NK...Dav7kn
  15 --HIERSIGEYIAARYRRAVEVGVGNNPEAAGLIAAA.....GALMLCTDIrpgIR...H.....
  16 -------ADYIAENYRGKVVEVGIGRFTAVAELLARR.....GFEVFATDV...VErraP.....
  17 ---------YIAENYRGKVVEVGIGRFTAVAELLARR.....GFEVFATDV...VErraP.....
  18 --YIETAIARFIAGRYRSVIEVGAGTNLHTANLLFRT.....GILIRCVDI...ID...Ppln..
  19 --------NYLLENPDLQILELGVGFYFEMALKLKQN.....NYNITVMDF...NQ...Eav7ny
  20 ---DLAEYILQHYPAGSRIIEVGIGRHPDTAELLSRYc....DFTCTDVMP...EG...P.....
  21 ---FAEFILTQATENPTRIVEIAVGKFDGVYQYLKRN.....ENIEIIKTD...IL...P.....
  22 ---------IASRVPKGKVVELGIGFQFKVALRLKEL.....GYDVLAVDW...NP...Asv7ge
  23 --ENFSEYIINNYQDSKKIIEVGVGKITEPSDILKKH.....LPNTTINLVd..IY...P.....
  24 ---------KRKVPNEGLIIEVGVGFYLKVAKKLKEY.....GFNVVVVDI...NQ...Eav7ik
  25 ----ETAVGRYIAANYRSAVEVGFGGKTTAAEIVQNA.....GIPVLCTDVha.YA...E.....
  26 ---DSEGALVDRLSSYDALVEVGVGNRPTVAAALDER.....GCRVTATDVdtcAV...P.....
  27 ----QEIAEFIRSHYTGRIIEIGVGQCGDVARLIPD-.....-LIATDIRP...VH...V.....
  28 -HSLAQDALVERFSSYTSAVEVGIGNRPAVAAALVSC.....GVDIVATDI...VScpvP.....
  29 ----------------SRVVEVGIGARPDVAAALAER.....GCAVTATDIeacTV...P.....


      0        60            70        80        90       100       110
     |         |             |         |         |         |         |
   1 SHGGIVRDDITSPR....MEIYRGAALIYSIRPPAEIHSSLMRVADAVGARLIIKPLTGEDIVTE
   2 SHGGIVRDDITSPR....MEIYRGAALIYSIRPPAEIHSSLMRVADAVGARLIIKPLTGEDIVTE
   3 TGLNAFYDDLFKPN....LEIYKNVGLIYSFRPPRDLQPFILEIAKKINCDLIIKALSGEEPIEE
   4 NGLNAFYDDLFEPN....FEIYKNVGLIYSFRPPRDLQPFILKIAKKLNCDLIIKALSGEEPIEE
   5 TGLNAFYDDLFNPD....LKIYKNVGLIYSFRPPRDLQPFILEIAKKINCNLIVKALSGEEPIEE
   6 NGLNAFYDDLFNPN....FEIYKNVGLIYSFRPPRDLQPFILEIAKKINCDLIVKALSGEEPIEK
   7 TWLPFARDDIFEPD....LSLYSGADVLYAIRPAEEMIPPLIDLAKKLDCDLVVYHLGFESYGDG
   8 LGLNAYKDDLFNPN....ISLYKNIDLIYSIRPPRDLQPYILDLSKKVNANLIIRPLLNEMPIKE
   9 LGLNAYKDDLFNPN....ISLYKNIDLIYSIRPPRDLQPYILDLSKKVNANLIIRPLLNEMPIKE
  10 LGLNAYKDDLFNPN....ISLYKNIDLIYSIRPPRDLQPYILDLSKKVNANLIIRPLLNEMPIKE
  11 QGIKGVVDDIFNPT....LGIYKDAKAIYSIRPAPEMMKPLLDLARKLKIPLYIVPLTGDRTPNG
  12 HGLNSKMDDIFKPD....LKIYKNIKLIYSIRPPRDLQPYLLNLSKNINCDLVIKPLSGEEPISE
  13 EGLNAFVDDIFNPK....LDIYKDADLIYSIRPPRDLQPFILNICKKYGISLLIKPLYGETPIND
  14 SGLNAEVDDIFNPN....ISLYMGAKAIYSIRPTPEMMNYILKISKAVKVPAYIVPLTGDPVPQG
  15 DGLTVVTDDVFEPD....LRLYEGADLIYAVRPGVEMVPPLIALADRIDSDLLVYHLGCEIYGDG
  16 EGCRFYVDDVTKPN....LKIYEGASLIYSLRPPPELFSAIVEVSRKVGADCLIKPLYGDYME--
  17 EGCRFYVDDVTKPN....LKIYEGASLIYSLRPPPELFSAIVEVSRKVGADCLIKPLYGDYME--
  18 SWIPYVKDDVSDPE....PGLYQGCDCIYAIRPVEEMIPPLIRLAHSVHADLVVYHLGFEGAARP
  19 LGLDAFKDDLFNPN....LKLYDSYDLMYSVRPPRDLQNDIARIAKLNDCNLIIQPLSNETALES
  20 EKLNYVRDDVFQPD....MRLYEGASLIYSIRPPVDLQDSIAAIANRVGADLLIRPFSSEKTDLS
  21 NDDEVIKDDITNPN....LELYENADIIYSIRPPSELQPHIERLSRKVDGTFIIKPLCNEDLNIS
  22 LGINAVRDDLFSPN....LELYRGVKALYSVRPTPEIVRSILELGKKLGVPVYILPLAGDVMPKT
  23 CNSDVIKDDITNPT....DKIYEDADLIYSIRPPEELQPDILKLSDKYNSDVIIKPLFTEEINFN
  24 ERIPGFVDDVFNPN....LKIYLKARAIYSIRPNPEIMMALLTLAKKVKVPLYIVPLSGDVPPRE
  25 GPVPSVVDDCVEPT....ISLYQAAGVIYAIRPGTEIVPALIELATRINADLIVYHLGFELYENG
  26 GTVRFVRDDVTDPD....VSVYSGAGAVYALNCPPELQRPLVSLASRVDADCLFTTLGGDPTLVD
  27 DGVKTVRDDIFNPS....EELYRGASLLYSIRPPIEVQIAMGDLALRIGADVLIRPLEDEIADLE
  28 PTVTFAYDDIVTTSeqraPDSVYDVELVYALNLPPELHRPFRDVADTVGADCRLTTLGYDAPIVP
  29 ETVRFVRDDVTDPE....RAVYEAADAVYALRCPPELQRAVVDVAGAVGAACYLTTLGGEPVVV-


             120       130   
              |         |   
   1 RKMKLVNYGRTYFYEYIAEVRSR
   2 RKMKLVNYGRTYFYEYIAEVRSR
   3 LKLVNYKGKPIYVW---------
   4 LKLVNYQGKPIYVW---------
   5 LKLVNYKGKPIYVW---------
   6 LKLVNYNGKPIYVW---------
   7 GTIVDCGVKLHYYYRHRSEP---
   8 LKLKNYKGEVFYI----------
   9 LKLKNYKGEVFYI----------
  10 LKLKNYKGEVFYI----------
  11 MKLINYKGIPIYKW---------
  12 LKLVNYFGKPLYIW---------
  13 LKLINYKGNALYC----------
  14 MKLITYRGIPIYKW---------
  15 GEVVDCGPALLHRYR--------
  16 ARIVNYKGAQFYL----------
  17 ARIVNYKGAQFYL----------
  18 APLPGCEVPLH------------
  19 LKPVCYNGK--------------
  20 RHFSEFR----------------
  21 SHKVKLK----------------
  22 MRLINYRGLAIY-----------
  23 FQ---------------------
  24 MKLINYKGISVYVW---------
  25 GERIVTDGVMLH-----------
  26 ATPETLPTQTLY-----------
  27 -----------------------
  28 CHPVSLPGGET------------
  29 -----------------------